[Bioperl-l] Bio::Tools::Genewise

Bill Dirks bdirks at uclink.berkeley.edu
Fri Mar 19 12:28:21 EST 2004

Thanks for your help.  I have wise 2.2.0 and the flag worked.  Now, I'm going to check out 

On Fri, 19 Mar 2004 12:14:02 -0500 (EST)
  Jason Stajich <jason at cgt.duhs.duke.edu> wrote:
>I think it is 2.2.0.  Note the ! lines.
>For those of you on linux biolinux.org provides a nice rpm install of wise
>[jason at lugano jason]$ genewise -help
>genewise ($Name: wise2-2-0 $)
>genewise <protein-file> <dna-file> in fasta format
>Dna sequence options
>  -u               start position in dna
>  -v               end position in dna
>  -trev            Compare on the reverse strand
>  -tfor [default]  Compare on the forward strand
>  -both            Both strands
>  -tabs            Report positions as absolute to truncated/reverse
>  -fembl            File is an EMBL file native format
>Protein comparison options
>  -s               start position in protein
>  -t               end   position in protein
>  -[g]ap    [ 12]  gap penalty
>  -[e]xt    [  2]  extension penalty
>  -[m]atrix [blosum62.bla]  Comparison matrix
>HMM options
>  -hmmer           Protein file is HMMer file (version 2 compatible)
>  -hname           Use this as the name of the HMM, not filename
>Gene Model options
>  -init   [default]  [default/global/local/wing/endbias] startend policy
>for the HMM/protein
>  -codon  [codon.table]  Codon file
>  -gene   [human.gf]  Gene parameter file
>  -subs   [1e-05] Substitution error rate
>  -indel  [1e-05] Insertion/deletion error rate
>  -cfreq  [model/flat] Using codon bias or not?     [default flat]
>  -splice [model/flat] Using splice model or GT/AG? [default model]
>  -intron [model/tied] Use tied model for introns   [default tied]
>  -null   [syn/flat]   Random Model as synchronous or flat [default syn]
>  -pg     <file>       Potential Gene file (heurestic for speeding
>  -alln   [1.0]   Probability of matching a NNN codon
>  -insert [model/flat] Use protein insert model     [default flat]
>Algorithm options
>  -alg    [623/623L/2193/2193L]  Algorithm used [default 623/623L]
>Output options [default -pretty -para]
>  -pretty          show pretty ascii output
>  -pseudo          Mark genes with frameshifts as pseudogenes
>  -genes           show gene structure
>!  -genesf          show gene structure with supporting evidence
>   -embl            show EMBL feature format with CDS key
>  -diana           show EMBL feature format with misc_feature key (for
>  -para            show parameters
>  -sum             show summary output
>  -cdna            show cDNA
>  -trans           show protein translation, breaking at frameshifts
>  -pep             show protein translation, splicing frameshifts
>  -ace             ace file gene structure
>  -gff             Gene Feature Format file
>  -gener           raw gene structure
>  -alb             show logical AlnBlock alignment
>  -pal             show raw matrix alignment
>  -block  [50]     Length of main block in pretty output
>  -divide [//]     divide string for multiple outputs
>New gene model statistics
>  -splice_max_collar      [5.0]  maximum Bits value for a splice site
>  -splice_min_collar      [-5.0] minimum Bits value for a splice site
>  -splice_score_offset    [4.5]  score offset for splice sites
>  -genestats              [gene.stat]
>Dynamic programming matrix implementation
>  -dymem      memory style [default/linear/explicit]
>  -kbyte      memory amount to use [4000]
>  -dydebug    drop into dynamite dp matrix debugger
>Standard options
>  -help      help
>  -version   show version and compile info
>  -silent    No messages on stderr
>  -quiet     No report on stderr
>  -erroroffstd No warning messages to stderr
>  -errorlog [file] Log warning messages to file
>See WWW help at http://www.sanger.ac.uk/Software/Wise2/
>On Fri, 19 Mar 2004, Ewan Birney wrote:
>> On Thu, 18 Mar 2004, Shawn Hoon wrote:
>> > You would need to add the -genesf option when running genewise.
>> >
>> > Also, you can check out the wrapper for genewise in
>> > Bio::Tools::Run::Genewise in the bioperl-run package.
>> I think -genesf is only available in the (now rather venerable) release
>> candidate Genewise at
>> http://www.sanger.ac.uk/Users/birney/wise2.2.3-rc7.tar.gz
>> The reason for not releasing this is that actually I need to back out the
>> changes made for the case of BLOSUM62.bla (it is in fact better to keep as
>> backwardly compatible as possible) which all comes down to the case
>> insanity that is Apple's HFS+ file system not playing nicely with cvs.
>> (yup. That was too much detail right?)
>> I will try to push the Wise2 package into some sort of sanity over this
>> month wrt to these things and then make a proper release. For the moment,
>> use the release candidate above...
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu

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